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"Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.

ABSTRACT: "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.

PROVIDER: PRJNA692426 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13443500.fastq.gz	Fastqsanger.gz
	SRR13486100.fastq.gz	Fastqsanger.gz
	SRR13443501.fastq.gz	Fastqsanger.gz
	SRR13486101.fastq.gz	Fastqsanger.gz
	SRR13443502.fastq.gz	Fastqsanger.gz

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"Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.

Project description:Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and accessibility. We uncover two TF groups that colocalize with most expressed factors, forming stripes in hierarchical clustering maps. The first group includes lineage-determining factors that occupy DNA elements broadly, consistent with their key role in tissue-specific transcription. The second one, dubbed universal stripe factors (USFs), comprises ∼30 SP, KLF, EGR, and ZBTB family members that recognize overlapping GC-rich sequences in all tissues analyzed. Knockouts and single-molecule tracking reveal that USFs impart accessibility to colocalized partners and increase their residence time. Mammalian cells have thus evolved a TF superfamily with overlapping DNA binding that facilitate chromatin accessibility.

| S-EPMC9481673 | biostudies-literature

"Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-07-21 | GSE164906 | GEO

Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Project description:Three-dimensional genome organization orchestrates recombination and transcription of immunoglobulin heavy chain (Igh) genes. The structure of wild type (WT) alleles includes a prominent architectural stripe that extends from a cluster of CTCF binding elements at the 3’ end of the locus (3’CBE), suggesting interactions of this end with sequences throughout the 2Mb Igh TAD. Here we elucidate interplay between regulatory elements located in the 3’Igh domain (260 kb) that impact the stripe. The CTCF-lacking intronic enhancer, Eì, promotes stripe formation and tethers sub-TADs between flanking CTCF-bound 3’CBE and IGCR1. Substituting Eì with an EF1á promoter in different orientations partially recapitulates epigenetic features of WT Igh alleles, including active histone modifications, sub-TAD formation and interactions with the 3’CBE, but does not restore VDJ recombination. Loss of IGCR1 increases the stripe while inverting the 3’CBE redirects the stripe away from the Igh locus. However, inverted 3’CBE continue to serve as a boundary against aberrant activation of genes outside the Igh domain by Eì. Our observations provide insights into mechanisms by which regulatory elements modulate chromatin structure and stripe formation.

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Functionality of stripe factors on chromatin accessibility (ATAC-Seq)

Project description:Functionality of stripe factors on chromatin accessibility (ATAC-Seq)

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Functionality of stripe factors on chromatin accessibility (ChIP-Seq)

Project description:Functionality of stripe factors on chromatin accessibility (ChIP-Seq)

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Functionality of stripe factors on chromatin accessibility (RNA-Seq)

Project description:Functionality of stripe factors on chromatin accessibility (RNA-Seq)

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Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

Project description:Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.

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RNA sequencing of stripe rust infected wheat leaves and isolated haustoria

Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections. Total RNA was extracted from a pool of stripe rust infected wheat leaves and from two biological replicates of haustoria isolates.

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NHLBI TOPMed: Partners HealthCare Biobank

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Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus

Project description:Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.

2023-03-29 | GSE223132 | GEO

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